It's not there anymore. It appears you have reorganized you site since I was last there.
How long before and how hard is it for you to statically link the binaries?
It would just take me doing the builds. Going static with the libs is trivial. I'm still working towards universal binary builds for OS X and it will probably not be until I get those done that I release a new full set of builds. At that point I'll release the new Linux binaries too. I suspect it will be at some point this week, or this weekend, when all of that happens.
And he coded cross-compatibility. Now if he would finish ogl enviroment mapping. 
New launcher and pilot code comes first. Then I'll start work on the GL code again.

8. Do all the directories have to be in lower case and without underscores to work on Linux?
Yes. Except for the underscore thing, that shouldn't be an issue (and if it is, I don't know about it).
9. In Linux, I installed to /usr/local/games/freespace2 and got the 'cannot find web curser' error. I ran the binary via a static link in /usr/local/bin. Do I need to make a script that cd's to the install dir, then run the real binary?
Yes, the game needs to be in the working directory when run. The best way to do this is with a shell script. I've always just used modified versions of startup scripts from Loki (the ones from Sam Lantinga). The one I included with the previous FS2_Open Linux installer was modified to use it's own GL libs if the system versions were too old.
10. Does fs2_open read the cd/dvd drive anymore?? I seem to remember when it would read all but root_fs2, sparky_fs2, and sparky_hi_fs2. Now it doesn't read anything. Can this be made to work again, in Linux and Windows?
It doesn't use the CD anymore. I had partially working code for the icculus.org version at one point, but it didn't allow you to easily eject and replace the CD under Linux. So, it never hit CVS. The main point of the previous code was not so much to allow CD use, but other filesystem use. You could even use an NFS/SMB mount to get to the VP files. At some point I plan to modify/complete that code and get it into FSO but that's just something I'll do when I'm *really* bored one day.
11. When I play FS_Port, the Media VP splash screen shows up instead of FS_Ports'; I am using Karajorma's first mod.ini.
The mod.ini files only work from the Launcher, the game knows nothing about them. So if you aren't running from the launcher then you'll have to specify the mod directories by hand (ie, "-mod fsport,mediavps").
The new launcher is going to introduce the idea of profiles. You can set up a profile for FSPort with all of the options and other game settings you want for that mod, including which binary to use, and easily run with those settings. Support for this will be at the game level too so you could setup a shellscript/shortcut with "launcher.exe -profile FSPort" and it would jump right to the game with all of the settings you like for the port. Or you could just do "fs2_open.exe -profile FSPort" and it will also use all of the profile settings, except for a different game binary. The profiles are stored in an ini file so you can either use the launcher to create/edit/delete the profiles or do it by hand in the ini file.
Oh and mod.ini files will still be usable with the new launcher, the launcher will inherit the settings from mod.ini for use by the profile, but they won't be at the game level like profiles will be. You can think of the profile.ini files as modular tables, you can have many of them and they will all be searched through for the profile that you want. They will basically be the new type of mod.ini file, except on steroids, and fully cross-platform.